Despite the many benefits that follow antiretroviral therapy (ART) initiation, its chronic use contributes to the early aging of people living with HIV/AIDS (PLWHA). The aim of this cross-sectional study was to trace the prevalence of and investigate possible renal, bone and metabolic changes, as well as cardiovascular risk in 94 asymptomatic PLWHA, relating them to the duration of ART use. Four groups were evaluated according to ART use: G1 (n = 21), ART-naïve individuals; G2 (n = 17), <2 years; G3 (n = 40), 2-10 years; and G4 (n = 16) on ART for more than 10 years. Our results showed a high prevalence of dyslipidemic individuals (64%), especially in those under ART. Lower creatine phosphokinase levels were observed in G1 as compared to the others (p < 0.05). Regarding the Framingham score, 12.1% of PLWHA showed moderate and high risk, and the highest proportion (38.5%) occurred in G4 (p = 0.003). A decrease in glomerular filtration rates occurred in 20% of patients, which was also more significant in G3 and G4 (p = 0.007). High prevalences of osteopenia and osteoporosis (53.2%) were found, especially in G1 and G4; however, G1 showed the lowest means for alkaline phosphatases (AP, p = 0.04 and BAP, p = 0.005) and osteocalcin (p = 0.005), in addition to higher vitamin-D concentrations (p = 0.04). Our study showed the possible contributory role of ART in these changes, which leads us to reflect on the need for specific conducts and patient care, pointing out the importance of individualized care in an attempt to increase life expectancy.